rnavigate.examples package

Subpackages

• rnavigate.examples.rmrp_data package
  • Module contents
• rnavigate.examples.rnasep_data package
  • Module contents
• rnavigate.examples.rrna_fragmap_data package
  • Module contents
• rnavigate.examples.tpp_data package
  • Module contents

Module contents

This module contains example rnav.Samples for different RNAs and data types.

TPP riboswitch in-vitro construct DMS-MaP data:

All sequences are based on PDB entry 3DHS. Except for the PDB file, all other data also contains structure cassettes. Data keywords:

pdb - 2GDI from the PDB ss - structure drawing diagram dmsmap - DMS-MaP structure probing data ringmap - RING-MaP correlations from DMS-MaP experiment pairprob - pairing probabilities using DMS-MaP as restraints

RNase P in-vitro construct SHAPE-MaP data

There are five samples here: common reference data shared between all RNase P samples variable name (rnasep_common) data keywords:

pdb - 3DHS, but with missing loops modelled in. shapejump - SHAPE-JuMP data ss_ct - 3DHS + cassettes, base-pairing structure with singlets removed ss_pdb - 3DHS, full base-pairing structure diagram pairprob - 3DHS + cassettes, pairing probabilities (sequence only)

4 experimental samples: 2 SHAPE reagents * 2 folding conditions variable names (rnasep_1, rnasep_2, rnasep_3, rnasep_4) data keywords:

all rnasep_common data keywords above + shapemap - 3DHS + cassettes, SHAPE-MaP experimental data ringmap - RING-MaP analysis on SHAPE-MaP data pairmap - PAIR-MaP analysis on SHAPE-MaP data

Example usage:

import rnavigate as rnav from rnavigate.examples import rnasep_1, rnasep_2

plot = rnav.plot_arcs(

samples=[rnasep_1, rnasep_2], sequence=”ss_pdb”, structure=”ss_pdb”, profile=”shapemap”, interactions=”ringmap”, )